Proteins solutions structure

Xia B, Tsui V, Case DA, Dyson J, Wright PE (2002) Comparison of protein solution structures refined by molecular dynamics simulations in vacuum, with a generalized Born model, and with explicit water, J Biomol NMR, 22 317-331... 

R. Pachter, R. B. Altman, and O. Jardetzky, /. Magn. Reson., 89, 578 (1990). The Dependence of a Protein Solution Structure on the Quality of the Input NMR Data. Application of the Double-Iterated Kalman Filter Technique to Oxytocin. 

J. F. Brinkley, R. B. Altman, B. S. Duncan, B. G. Buchanan, and O. Jardetzky. 1988. Heuristic refinement method for the derivation of protein solution structures validation on cytochrome b562. Journal of Chemical Information and Computer Sciences 28(4) 194-210. 

Lin CH et al (2001) A small domain of CBP/p300 binds diverse proteins solution structure and functional studies. Mol Cell 8(3) 581-590... 

Since the first protein solution structure was determined by high resolution NMR spectroscopy about 25 years ago [166], NMR has been estabhshed as the only experimental method that provides both structural and dynamical information at atomic resolution close to physiologically relevant conditions. Protein structure determination in living cells has also been achieved recently by in-cell NMR [18]. However, the limitation of this technique in structural studies hes in low sensitivities and poor resolution when the size of macromolecules increases. Some proteins, in particular metalloproteins, might not be stable for a period of time (days or weeks) or have limited solubility. Moreover, new challenges in fife science have also promoted development of new NMR methods which will improve sensitivities and reduce acquisition times to fulfil the requirement of characterization of these proteins and their complexes. 

P. D. Thomas, V. J. Basus, and T. L. James, Proc. Natl. Acad. Sci. U.S.A., 88, 1237 (1991). Protein Solution Structure Determination Using Distances from Two-Dimensional Nuclear Overhauser Effect Experiments Effect of Approximations on the Accuracy of Derived Structures. 

Iwahara et al have shown that Mn(II)-EDTA-derivatized deoxythymidine, incorporated into DNA, can provide a site of paramagnetic labeling that can be used to ascertain the polarity of protein binding to DNA. The label also provides long range distance constraints for the refinement of nucleotide/protein solution structures. The authors point out that by using different metal ions, the method can be optimized for intermolecular distance ranges between 9 and 35 A. 

Traditionally, least-squares methods have been used to refine protein crystal structures. In this method, a set of simultaneous equations is set up whose solutions correspond to a minimum of the R factor with respect to each of the atomic coordinates. Least-squares refinement requires an N x N matrix to be inverted, where N is the number of parameters. It is usually necessary to examine an evolving model visually every few cycles of the refinement to check that the structure looks reasonable. During visual examination it may be necessary to alter a model to give a better fit to the electron density and prevent the refinement falling into an incorrect local minimum. X-ray refinement is time consuming, requires substantial human involvement and is a skill which usually takes several years to acquire. 

FeMoco can be extracted from the MoFe protein into A(-methylfor-mamide (NMF) solution 32) and has been analyzed extensively using a wide range of spectroscopic techniques both bound to the protein and in solution after extraction from it (33). The extracted FeMoco can be combined with the MoFe protein polypeptides, isolated from strains unable to synthesize the cofactor, to generate active protein. The structure of the FeMoco is now agreed 4, 5, 7) as MoFeTSg homocitrate as in Fig. 4. FeMoco is bound to the a subunit through residues Cys 275, to the terminal tetrahedral iron atom, and His 442 to the molybdenum atom (residue numbers refer to A. vinelandii). A number of other residues in its environment are hydrogen bonded to FeMoco and are essential to its activity (see Section V,E,2). The metal... 

Contact shifts give information on the electronic structure of the iron atoms, particularly on the valence distribution and on the magnetic coupling within polymetallic systems. The magnetic coupling scheme, which is considered later, fully accounts for the variety of observed hyperfine shifts and the temperature dependence. Thus, through the analysis of the hyperfine shifts, NMR provides detailed information on the metal site(s) of iron-sulfur proteins, and, thanks to the progress in NMR spectroscopy, also the solution structure 23, 24 ). 

The solution structure determination of iron-sulfur proteins is feasible in most cases. To achieve this result, it is necessary to have enough structural constraints to make it possible to obtain a family of conformers with similar folding from many randomly generated structures (95). 

Table III reports structural statistics relative to the solution structures of iron-sulfur proteins available from the Protein Data Bank (118). The lowest percentage of residue assignment occurs for oxidized Synechococcus elongatus Fd (119). The highest percentage of proton assignment is instead obtained for oxidized E. halophila HiPIP, with a value as high as 95% (120). A close figure was also obtained for the reduced protein (94%). In the latter case, such high values are obtained also thanks to the availability of labeled...

NMR Assignments, Structural Constraints, and Structural Parameters for the Available NMR Solution Structures of Iron-Sulfur Proteins"- ... 

While crystal structures of rubredoxins have been known since 1970 (for a full review on rubredoxins in the crystalline state, see Ref. (15)), only recently have both crystal and solution structures of Dx been reported (16, 17) (Fig. 3). The protein can be described as a 2-fold symmetric dimer, firmly hydrogen-bonded and folded as an incomplete /3-barrel with the two iron centers placed on opposite poles of the molecule, 16 A apart. Superimposition of Dx and Rd structures reveal that while some structural features are shared between these two proteins, significant differences in the metal environment and water structure exist. They can account for the spectroscopic differences described earlier. 

Numerous organisms, both marine and terrestrial, produce protein toxins. These are typically relatively small, and rich in disulfide crosslinks. Since they are often difficult to crystallize, relatively few structures from this class of proteins are known. In the past five years two dimensional NMR methods have developed to the point where they can be used to determine the solution structures of small proteins and nucleic acids. We have analyzed the structures of toxins II and III of RadiarUhus paumotensis using this approach. We find that the dominant structure is )9-sheet, with the strands connected by loops of irregular structure. Most of the residues which have been determined to be important for toxicity are contained in one of the loops. The general methods used for structure analysis will be described, and the structures of the toxins RpII and RpIII will be discussed and compared with homologous toxins from other anemone species. 

Lucke C., Franzoni L., Abbate F., Lohr F., et al. (1999). Solution structure of a recombinant mouse major urinary protein. Eur J Biochem 266, 1210-1218. 

Because protein ROA spectra contain bands characteristic of loops and turns in addition to bands characteristic of secondary structure, they should provide information on the overall three-dimensional solution structure. We are developing a pattern recognition program, based on principal component analysis (PCA), to identify protein folds from ROA spectral band patterns (Blanch etal., 2002b). The method is similar to one developed for the determination of the structure of proteins from VCD (Pancoska etal., 1991) and UVCD (Venyaminov and Yang, 1996) spectra, but is expected to provide enhanced discrimination between different structural types since protein ROA spectra contain many more structure-sensitive bands than do either VCD or UVCD. From the ROA spectral data, the PCA program calculates a set of subspectra that serve as basis functions, the algebraic combination of which with appropriate expansion coefficients can be used to reconstruct any member of the... 

Lerche, M.H. and Poulsen, F.M. (1998) Solution structure of barley lipid transfer protein complexed with palmitate. Two different binding modes of palmitate in the homologous maize and barley nonspecific lipid transfer proteins. Protein Science 7, 2490-2498. 

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